Does anyone have any suggestions of large open source projects with high quality code that would be good to study.
Scott Hanselman has been reviewing applications and their respective source code in a series "The Weekly Source Code". Pretty in depth and diverse stuff.
See the thread pointed by Alexander for C# projects. For Java, I'd recommend Spring Framework. It's a big, well managed project with good documentation and very clean (even if somewhat verbose) code.
Community Server is fairly substantial for an ASP.NET app and well written. It's sourcecode can be viewed online: http://code.communityserver.org/
In Java-land, Apache Mina and Stripes are two projects that come to mind. While I haven't actually hacked their source codes, I get a warm and fuzzy feeling that these frameworks are well built when I use them.
Before writing the Stripes book, I read pretty much all of the source code for Stripes to learn it inside out. I was very impressed by the quality of the code at all levels: design, extensibility, interfaces/implementation decoupling, documentation...everything is top notch.